6PZ2

Crystal Structure of FolP (dihydropteroate synthase) from Colstridium difficile in the presence of pteroic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HB7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	2.4-2.6 M ammonium sulfate, 200 mM LiCl, 100 mM CHES (pH 9), 4 mM pteroic acid

Crystal Properties
Matthews coefficient	Solvent content
5.01	75.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.258	α = 90
b = 156.258	β = 90
c = 84.708	γ = 120

Symmetry
Space Group	P 63 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210r		2018-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.99861	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	50	99.2	0.098	45.4	13		41365

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	99.5		0.454	4.3	7.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4hb7	2	37.56	39244	2116	98.93	0.1895	0.1876	0.2238	RANDOM	39.817

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-1.63	-0.81		-1.63		5.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.698
r_dihedral_angle_3_deg	15.964
r_dihedral_angle_4_deg	15.207
r_dihedral_angle_1_deg	6.493
r_angle_refined_deg	1.753
r_angle_other_deg	0.549
r_chiral_restr	0.076
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.698
r_dihedral_angle_3_deg	15.964
r_dihedral_angle_4_deg	15.207
r_dihedral_angle_1_deg	6.493
r_angle_refined_deg	1.753
r_angle_other_deg	0.549
r_chiral_restr	0.076
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2061
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	81

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.